pseudobulk

Nextflow workflow for pseudobulking single-cell count matrices

Prerequisites:

• Nextflow
• Singularity

An example of the nextflow run script is in run.sh

Parameters:

• --samples TSV containing the sample IDs and data files (examples: assets/input_examples/samples)
• --GE-threshold percent of individuals that must express the gene to keep it in the pseudobulk (default: 30)
• --individual-cell-threshold minimum number of cells an individual must have to be included in the pseudobulk (default: 15)
• --pseudobulk-cell-threshold minimum number of cells a cell type must have to pseudobulk it (default: 2000)
• --outdir name of the output directory

Outputs:

• pseudobulks.[meta/annot] contains the unfiltered, filtered, and filtered + transformed pseudobulks
• pseudobulk_summary contains metadata about the pseudobulks